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Theodosius Dobzhansky Center for Genome Bioinformatics

Invited researcher Stephen James O’Brien
Contract number
11.G34.31.0068
Time span of the project
2011-2015

As of 30.01.2020

21
Number of staff members
154
scientific publications
1
Objects of intellectual property
General information

Name of the project: Creation of a laboratory for research in genomics and bioinformatics at the Saint Petersburg State University with the research topic: «Biology. Bioinformatics. Biomedical technologies. Ethics. Environmental protection»

Strategy for Scientific and Technological Development Priority Level: а


Goals and objectives

Research directions: Biology, bioinformatics, biomedical technologies, ethics, environmental protection

Project objective:

- Creation of the Center for Genome Bioinformatics in Saint Petersburg for interdisciplinary research (genetics, mathematics, programming and other domains) as well as for training students and interns.

- Development and implementation of innovative computer and bioinformatics tools for analysis with application of the most recent achievements in genetics, bioinformatics and computer biology for assembling genomes of living organisms, their annotation and detecting genes with subsequent implementation of produced results in health care, agriculture and environmental protection.


The practical value of the study

  • Development and implemented the GWATCH information platform for visualization and interpretation of results of the search for genes based on whole genome association analysis.
  • The «Russian genomes» project of the Saint Petersburg State University has been launched. Within the project, 334 whole genomes of people living in various regions of Russia have been sequenced.
  • Creation of a Russian bioinformatics database based on research of the genetic variety of Russian populations and a genetic database containing medically significant genome variations in Russian populations
  • Creation of the GMTV program and database that is aimed at cataloging and analysis of Mycobacterium tuberculosis strains from the territory of Russia.
  • For the first time we have sequenced, assembled and annotated genomes of several species of plants, detected a number of genes whose functions are associated with various types of sexual and asexual reproduction, we are conducting further genome research of reproduction regulation.
  • We have collected a bank of biological samples of mammals living on the territory of Russia.
  • New methods and tools have been developed for analysis of data of genome sequencing of over 40 species of rare animals and plants including the cheetah, the African wolf and the highly heterozygous plant Boechera.

Implemented results of research:

  • The GWATCH information platform has been launched in the field of bioinformatics and genetics. The system contains an innovative set of interactive programs automating detection and checking of gene variations that mediates resistivity against human chronic illnesses. In this regard GWATCH is a complex but user-friendly computational program for viewing gene associations, explicit confirmation new gene associations and determining important impact of genes that were hard to detect before.
  • Obtained results can be used to search for new genes associated with diseases, for monitoring onset of such diseases as AIDS and tuberculosis as well as for development of the evolutionary theory of genesis of species and bioinformatics as a domain of science.

Education and career development:

  • We have developed the course «Introduction to bioinformatics» at the Saint Petersburg at the Saint Petersburg State University in Russian for the Coursera international education platform.
  • We have conducted seminars with participation of researchers in adjacent domains.
  • The Laboratory has provided consulting and internships for students of foreign universities.
  • We have organized internships for members of the academic staff of the Laboratory at the Far Eastern Federal University, the Bashkir State University (Russia).

Collaborations: Smithsonian Institution (USA), Harvard University (USA), Duke University in North Carolina (USA), Federal University of Rio Grande do Sul (Brazil), University of Pretoria (South Africa), University of Porto (Portugal), University of Zurich (Switzerland), Central European Institute of Technology – CEITEC, Masaryk University (Czech Republic), Indian Institute of Technology Madras (India), Peking University (China PR): joint study of bioinformatics data, collaborative publications

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Dobrynin P., Liu S., Tamazian G., Xiong Z., Yurchenko A.A., et al
Genomic Legacy of the African Cheetah, Acinonyx Jubatus. Genome Biology 16: 277 (2015).
Svitin A., Malov S., Cherkasov N., et al.
GWATCH: a Web Platform for Automated Gene Association Discovery Analysis. GigaScience 3(1): 18 (2014).
Tamazian T., Simonov S., Dobrynin P., et al.
Annotated Features of the Domestic Cat (Felis catus) Genome. GigaScience 3(13): 3 (2014).
Harper C.K, Ludwig A., Clarke A.B., et al.
Robust Forensic Matching of Confiscated Horns and Tissues to Individual Poached African Rhinoceros. Current Biology 28(1): R13–R14 (2018).
Koepfli K.P., Pollinger J., Robinson J., et al.
Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species. Current Biology 25(16): 2158–165 (2015)
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